Latest improvements for QIAGEN CLC Main Workbench

Improvements

• Loading reports with very large tables takes less time.
• Various minor improvements

Bug fixes

• Fixed an issue causing Standard Import of GenBank format to import qualifiers’ values as annotations surrounded by quotes. The surrounding quotes are now removed.
• Fixed an issue causing GFF3 export to fail when sequence annotations included features with incorrectly formatted frame qualifiers. Now, such frame qualifiers are ignored.

Data related updates

From September 19, 2023, Download Pfam Database downloads Pfam 36.0. This update also affects download using earlier versions of the CLC Main Workbench.

Advanced notice

We plan to remove the Pause and Resume options, available for some processes in the Workbench, in a future release. If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• Download BLAST Databases is more resilient to interrupted connections and similar issues when downloading large databases.

Advance notice

We plan to remove the Pause and Resume options, available for some processes in the Workbench, in a future release. If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Bug fixes

• Fixed an issue that caused Join Alignments to fail in CLC Main Workbench 23.0.1 and 23.0.2.
• Fixed an issue that caused the value selection range of gradient sliders in the Side Panel to be displayed incorrectly when using Locale Settings that do not use ‘.’ (dot) as a decimal separator.
• Fixed an issue where lines in pdfs containing history information were not wrapped, resulting in the ends of long lines not being present in the exported document.

Bug fixes

• Fixed an issue that caused fragment lengths to be incorrect in tables from Design Primers. The values are re-calculated when a table is opened, hence previous designs do not need to be repeated.
• Fixed a rare issue where Rebuild Index could not repair a corrupt search index.
• Various minor bug fixes

Bug fixes

• Fixed an issue where dates indicated with forward slashes in CSV format files were not recognized as dates by Import Metadata.
• Fixed an issue where the history entry in a sequence list after sorting always stated the sorting was based on length, even the sorting was based on name or marked status.
• Fixed an issue causing Annotate with GFF/GTF/GVF file to fail when the option “Ignore duplicate annotation” was checked.
• Fixed an issue causing Standard Import of GenBank format to stall if qualifier names spanned more than one line.

Please see the release notes for CLC Main Workbench 23.0, below, for a full list of changes since the last general release of this software.

New features

• Homology Based Cloning – A new tool for designing cloning experiments for cloning methods relying on homologous ends, such as Gibson Assembly®.
• Annotate with GFF/GVF/GTF file – A tool for adding annotations from a GFF, GVF or GTF format file onto sequences, individual or in sequence lists. This tool was formerly distributed in the Annotate with GFF file plugin.
• A Welcome Center is presented when the Workbench is first started up. It provides quick links to information to help when getting started, including links to manuals, tutorials, and quick tips.

Improvements

Sequence Lists

• Checkboxes can be enabled to select sequences within the graphical view of sequence lists. Lists can be sorted based on whether they are marked or not, and marked sequences can be deleted.
• In the Annotation Table view, the following changes have been made to the right-click menu:
  • The underlying sequence of selected annotations can be deleted.
  • Names of sequences selected annotations are on can be copied to the clipboard.
  • The option to export to gff now exports to GFF3 format – Export Selected to GFF3 File. This option has also been updated in the Annotation Table view of individual sequence elements.
• In the Table view, selected sequences can be deleted, and the names of selected sequences can be copied.
• Various minor improvement to labels in right-click menus.

CLC Metadata Tables

• When launching analyses in Batch mode, or when launching workflows with an Iterate element, CLC Metadata Tables with data associated can be used directly as input. Each row in the CLC Metadata Table is a batch unit, with data elements associated to a row, of a type compatible as input to the analysis, being the default contents of a batch unit. When launching workflows, the column to base the batch units on can be specified.
• New options for editing CLC Metadata Tables, including for adding content from other CLC Metadata Tables or Excel, CSV or TSV files. Rows in a CLC Metadata Table can also be selected and used to make a new CLC Metadata Table.
• When associating data automatically to CLC Metadata Tables, a preview of the associations that will be made is shown in the wizard.

Read mappings

• The “Disconnect paired reads” viewing option for read mappings has been replaced by the option “Show strands of paired reads”. The behaviour of the new option is like the old one except that the members of each pair are connected by a blue line.
• A  “Match coloring” side panel provides the colors applied to reads when the compactness level is set to “Packed”.
• Deletions are now highlighted in the coverage graph and in the shown reads.
• Assemble Sequences to Reference supports alignment of reads that span the origin of a circular reference.

Import and export

• GFF3 Export retains the case of attribute headers. Previously, all headers were adjusted to lower case during export.
• Standard Import can be used to import files from AWS S3 locations.
• When exporting images to bitmap-based formats, the Screen resolution and High resolution options are now bounded so the maximum supported number of pixels will not be exceeded.
• Workflow Export elements can be preconfigured to export to locations on AWS S3.

Other improvements

• Search for Sequences at UniProt has been substantially updated and improved. Changes include new search fields and more informative information returned, including links to PubMed entries.
• Quick Search and Local Search have been substantially improved. Please refer to the documentation for details.
• Secondary Peak Calling has a new option “Peak detection stringency”
• Updated restriction site database to REBASE 2022-06-30.
• The overview of batch units when launching tools or workflows in Batch mode and when launching workflows with control flow elements (Iterate, Collect and Distribute), have been aligned. In the latter, the contents of batch units can now be adjusted by including or excluding elements based on a part of their name. Previously this was only possible when launching analyses in Batch mode. Right-click options to remove batch units or to remove particular data elements from a batch unit, have been removed.
• Workflows containing containing Split Sequence List elements can be run in Batch mode.
• A button has been added to the top Toolbar for contacting our Support team.
• Various minor improvements

Bug fixes

Workflow related

• Fixed an issue affecting the location of outputs generated from a workflow element that was also linked to a Collect and Distribute element. In cases where the output folder name was defined using the {input} or {2} placeholder, these outputs were sometimes all saved to the first folder created, instead of to different folders as intended.
• Fixed an issue where default names were applied to outputs from Output elements attached directly to an Iterate element in workflows, even when naming placeholders had been configured.
• Fixed an issue affecting workflows with nested Iterate elements where results from the outer level of iteration flowed into a Distribute and Collect element. Any output elements generated in the inner iteration, which should have saved, were lost.
• Fixed an issue where unlocked options for on-the-fly importers in a workflow would be locked if the Input element was re-opened for editing.
• Fixed an issue affecting the “Highlight used elements” view setting of the workflow editor, where most elements, not just the unconnected ones, were grayed out when this option was selected.

Other bug fixes

• Fixed an issue causing Show Enzymes Cutting Inside/Outside Selection to give wrong results when the selection crossed the junction of a circular sequence and a desired number of cut sites outside the selection was not specified.
• Fixed an issue that could cause the Workbench to freeze when exporting elements with certain view settings to graphics formats, for example read mappings with compactness set to “Not compact” and the Sequence layout set to “No wrap”.
• Fixed an issue affecting hyperlinked table entries, where html tags were sometimes included as text in the information exported to Excel or CSV formats.
• Fixed an issue where upgrading on Windows systems could be blocked due to a locked file.
• Fixed an issue where text in installer screens was not visible when installing the software in ‘dark mode’ on Linux.
• Various minor bug fixes

Changes

• The Cloning tool has been renamed to Restriction Based Cloning.
• The “Disconnect paired reads” viewing option for read mappings has been replaced by the option “Show strands of paired reads”. The behaviour of the new option is like the old one except that the members of each pair are connected by a blue line.
• Indexes used for searching are not the same as the ones used in earlier versions. New indexes are automatically established for each available CLC Workbench Location when installing version 23.0 for the first time. So for Workbenches, this change will be seamless in most cases. However, if you later run an old version of a CLC Workbench and save new data elements to a CLC Workbench location, a search from the newer version of the software will not find those unless you manually re-index your CLC Workbench locations.
• When tools or workflows are run in Batch mode, “Create subfolders per batch unit” is selected by default. Previously this option was not selected by default.
• PFAM accessions in the results table created by PFAM Domain Search are linked to PFAM entries hosted by InterPro. Links generated in older versions of the software were to the Pfam website, which is being decommissioned.
• AWS Connections:
  • An AWS region can be specified in the AWS connection settings. When upgrading from an earlier version with AWS connections already defined, the region will be set to us-east-1 by default. This can be changed by editing the connection. The region setting is primarily relevant if you plan to submit analyses from a CLC Workbench with the CLC Cloud Module installed to run on a CLC Genomics Cloud setup.
  • Information about AWS Connections now includes whether the connection is valid for submitting jobs to a CLC Genomics Cloud, in addition to whether the connection is valid for accessing files on AWS S3.
• The Java version bundled with CLC Main Workbench 23.0 Java 17.0.4, where we use the JRE from the Azul OpenJDK builds.

Functionality retirement

Batch Rename (legacy) has been retired.

Plugin notes

Plugin retirements

• Annotate with GFF file plugin The tool Annotate with GFF/GVF/GTF file is now available directly in the WB.